Generates gbarplots for ASEset objects. Two levels of plotting detail are
provided: a detailed gbarplot of read counts by allele useful for fewer
samples and SNPs, and a less detailed gbarplot of the fraction of imbalance,
useful for more samples and SNPs.
This function serves the same purpose as the normal barplot, but with
trellis graphics using lattice, to be able to integrate well with Gviz track
functionality.
Author(s)
Jesper R. Gadin
See Also
The ASEset class which the gbarplot
function can be called up on.
The barplot non trellis
barplot.
Examples
data(ASEset)
gbarplot(ASEset[1])
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(AllelicImbalance)
Loading required package: grid
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GenomicAlignments
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/AllelicImbalance/ASEset-gbarplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ASEset-gbarplot
> ### Title: gbarplot ASEset objects
> ### Aliases: ASEset-gbarplot gbarplot gbarplot,ASEset-method
> ### Keywords: gbarplot
>
> ### ** Examples
>
>
> data(ASEset)
> gbarplot(ASEset[1])
>
>
>
>
>
>
> dev.off()
null device
1
>